File: lammps.py

package info (click to toggle)
lammps 0~20181211.gitad1b1897d%2Bdfsg1-1~bpo9%2B1
  • links: PTS, VCS
  • area: main
  • in suites: stretch-backports
  • size: 318,868 kB
  • sloc: cpp: 729,569; python: 40,508; xml: 14,919; fortran: 12,142; ansic: 7,454; sh: 5,565; perl: 4,105; f90: 2,700; makefile: 2,114; objc: 238; lisp: 163; tcl: 61; csh: 16; awk: 14
file content (1128 lines) | stat: -rw-r--r-- 36,753 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
# ----------------------------------------------------------------------
#   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
#   http://lammps.sandia.gov, Sandia National Laboratories
#   Steve Plimpton, sjplimp@sandia.gov
#
#   Copyright (2003) Sandia Corporation.  Under the terms of Contract
#   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
#   certain rights in this software.  This software is distributed under
#   the GNU General Public License.
#
#   See the README file in the top-level LAMMPS directory.
# -------------------------------------------------------------------------

# Python wrappers on LAMMPS library via ctypes

# for python3 compatibility

from __future__ import print_function

# imports for simple LAMMPS python wrapper module "lammps"

import sys,traceback,types
from ctypes import *
from os.path import dirname,abspath,join
from inspect import getsourcefile

# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"

from collections import namedtuple
import os
import select
import re
import sys

def get_ctypes_int(size):
  if size == 4:
    return c_int32
  elif size == 8:
    return c_int64
  return c_int

class MPIAbortException(Exception):
  def __init__(self, message):
    self.message = message

  def __str__(self):
    return repr(self.message)

class lammps(object):

  # detect if Python is using version of mpi4py that can pass a communicator

  has_mpi4py = False
  try:
    from mpi4py import MPI
    from mpi4py import __version__ as mpi4py_version
    if mpi4py_version.split('.')[0] in ['2','3']: has_mpi4py = True
  except:
    pass

  # create instance of LAMMPS

  def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
    self.comm = comm
    self.opened = 0

    # determine module location

    modpath = dirname(abspath(getsourcefile(lambda:0)))
    self.lib = None

    # if a pointer to a LAMMPS object is handed in,
    # all symbols should already be available

    try:
      if ptr: self.lib = CDLL("",RTLD_GLOBAL)
    except:
      self.lib = None

    # load liblammps.so unless name is given
    #   if name = "g++", load liblammps_g++.so
    # try loading the LAMMPS shared object from the location
    #   of lammps.py with an absolute path,
    #   so that LD_LIBRARY_PATH does not need to be set for regular install
    # fall back to loading with a relative path,
    #   typically requires LD_LIBRARY_PATH to be set appropriately

    if not self.lib:
      try:
        if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
        else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
                              RTLD_GLOBAL)
      except:
        if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
        else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)

    # define ctypes API for each library method
    # NOTE: should add one of these for each lib function

    self.lib.lammps_extract_box.argtypes = \
      [c_void_p,POINTER(c_double),POINTER(c_double),
       POINTER(c_double),POINTER(c_double),POINTER(c_double),
       POINTER(c_int),POINTER(c_int)]
    self.lib.lammps_extract_box.restype = None

    self.lib.lammps_reset_box.argtypes = \
      [c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
    self.lib.lammps_reset_box.restype = None

    self.lib.lammps_gather_atoms.argtypes = \
      [c_void_p,c_char_p,c_int,c_int,c_void_p]
    self.lib.lammps_gather_atoms.restype = None

    self.lib.lammps_gather_atoms_concat.argtypes = \
      [c_void_p,c_char_p,c_int,c_int,c_void_p]
    self.lib.lammps_gather_atoms_concat.restype = None

    self.lib.lammps_gather_atoms_subset.argtypes = \
      [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
    self.lib.lammps_gather_atoms_subset.restype = None

    self.lib.lammps_scatter_atoms.argtypes = \
      [c_void_p,c_char_p,c_int,c_int,c_void_p]
    self.lib.lammps_scatter_atoms.restype = None

    self.lib.lammps_scatter_atoms_subset.argtypes = \
      [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
    self.lib.lammps_scatter_atoms_subset.restype = None

    # if no ptr provided, create an instance of LAMMPS
    #   don't know how to pass an MPI communicator from PyPar
    #   but we can pass an MPI communicator from mpi4py v2.0.0 and later
    #   no_mpi call lets LAMMPS use MPI_COMM_WORLD
    #   cargs = array of C strings from args
    # if ptr, then are embedding Python in LAMMPS input script
    #   ptr is the desired instance of LAMMPS
    #   just convert it to ctypes ptr and store in self.lmp

    if not ptr:

      # with mpi4py v2, can pass MPI communicator to LAMMPS
      # need to adjust for type of MPI communicator object
      # allow for int (like MPICH) or void* (like OpenMPI)

      if comm:
        if not lammps.has_mpi4py:
          raise Exception('Python mpi4py version is not 2 or 3')
        if lammps.MPI._sizeof(lammps.MPI.Comm) == sizeof(c_int):
          MPI_Comm = c_int
        else:
          MPI_Comm = c_void_p

        narg = 0
        cargs = 0
        if cmdargs:
          cmdargs.insert(0,"lammps.py")
          narg = len(cmdargs)
          for i in range(narg):
            if type(cmdargs[i]) is str:
              cmdargs[i] = cmdargs[i].encode()
          cargs = (c_char_p*narg)(*cmdargs)
          self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
                                           MPI_Comm, c_void_p()]
        else:
          self.lib.lammps_open.argtypes = [c_int, c_int, \
                                           MPI_Comm, c_void_p()]

        self.lib.lammps_open.restype = None
        self.opened = 1
        self.lmp = c_void_p()
        comm_ptr = lammps.MPI._addressof(comm)
        comm_val = MPI_Comm.from_address(comm_ptr)
        self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))

      else:
        if lammps.has_mpi4py:
          from mpi4py import MPI
          self.comm = MPI.COMM_WORLD
        self.opened = 1
        if cmdargs:
          cmdargs.insert(0,"lammps.py")
          narg = len(cmdargs)
          for i in range(narg):
            if type(cmdargs[i]) is str:
              cmdargs[i] = cmdargs[i].encode()
          cargs = (c_char_p*narg)(*cmdargs)
          self.lmp = c_void_p()
          self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
        else:
          self.lmp = c_void_p()
          self.lib.lammps_open_no_mpi(0,None,byref(self.lmp))
          # could use just this if LAMMPS lib interface supported it
          # self.lmp = self.lib.lammps_open_no_mpi(0,None)

    else:
      # magic to convert ptr to ctypes ptr
      if sys.version_info >= (3, 0):
        # Python 3 (uses PyCapsule API)
        pythonapi.PyCapsule_GetPointer.restype = c_void_p
        pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
        self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
      else:
        # Python 2 (uses PyCObject API)
        pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
        pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
        self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))

    # optional numpy support (lazy loading)
    self._numpy = None

    # set default types
    self.c_bigint = get_ctypes_int(self.extract_setting("bigint"))
    self.c_tagint = get_ctypes_int(self.extract_setting("tagint"))
    self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
    self._installed_packages = None

  # shut-down LAMMPS instance

  def __del__(self):
    if self.lmp and self.opened:
      self.lib.lammps_close(self.lmp)
      self.opened = 0

  def close(self):
    if self.opened: self.lib.lammps_close(self.lmp)
    self.lmp = None
    self.opened = 0

  def version(self):
    return self.lib.lammps_version(self.lmp)

  def file(self,file):
    if file: file = file.encode()
    self.lib.lammps_file(self.lmp,file)

  # send a single command

  def command(self,cmd):
    if cmd: cmd = cmd.encode()
    self.lib.lammps_command(self.lmp,cmd)

    if self.has_exceptions and self.lib.lammps_has_error(self.lmp):
      sb = create_string_buffer(100)
      error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
      error_msg = sb.value.decode().strip()

      if error_type == 2:
        raise MPIAbortException(error_msg)
      raise Exception(error_msg)

  # send a list of commands

  def commands_list(self,cmdlist):
    cmds = [x.encode() for x in cmdlist if type(x) is str]
    args = (c_char_p * len(cmdlist))(*cmds)
    self.lib.lammps_commands_list(self.lmp,len(cmdlist),args)

  # send a string of commands

  def commands_string(self,multicmd):
    if type(multicmd) is str: multicmd = multicmd.encode()
    self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))

  # extract lammps type byte sizes

  def extract_setting(self, name):
    if name: name = name.encode()
    self.lib.lammps_extract_atom.restype = c_int
    return int(self.lib.lammps_extract_setting(self.lmp,name))

  # extract global info

  def extract_global(self,name,type):
    if name: name = name.encode()
    if type == 0:
      self.lib.lammps_extract_global.restype = POINTER(c_int)
    elif type == 1:
      self.lib.lammps_extract_global.restype = POINTER(c_double)
    else: return None
    ptr = self.lib.lammps_extract_global(self.lmp,name)
    return ptr[0]

  # extract global info

  def extract_box(self):
    boxlo = (3*c_double)()
    boxhi = (3*c_double)()
    xy = c_double()
    yz = c_double()
    xz = c_double()
    periodicity = (3*c_int)()
    box_change = c_int()

    self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
                                byref(xy),byref(yz),byref(xz),
                                periodicity,byref(box_change))

    boxlo = boxlo[:3]
    boxhi = boxhi[:3]
    xy = xy.value
    yz = yz.value
    xz = xz.value
    periodicity = periodicity[:3]
    box_change = box_change.value

    return boxlo,boxhi,xy,yz,xz,periodicity,box_change

  # extract per-atom info
  # NOTE: need to insure are converting to/from correct Python type
  #   e.g. for Python list or NumPy or ctypes

  def extract_atom(self,name,type):
    if name: name = name.encode()
    if type == 0:
      self.lib.lammps_extract_atom.restype = POINTER(c_int)
    elif type == 1:
      self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int))
    elif type == 2:
      self.lib.lammps_extract_atom.restype = POINTER(c_double)
    elif type == 3:
      self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
    else: return None
    ptr = self.lib.lammps_extract_atom(self.lmp,name)
    return ptr

  @property
  def numpy(self):
    if not self._numpy:
      import numpy as np
      class LammpsNumpyWrapper:
        def __init__(self, lmp):
          self.lmp = lmp

        def _ctype_to_numpy_int(self, ctype_int):
          if ctype_int == c_int32:
            return np.int32
          elif ctype_int == c_int64:
            return np.int64
          return np.intc

        def extract_atom_iarray(self, name, nelem, dim=1):
          if name in ['id', 'molecule']:
            c_int_type = self.lmp.c_tagint
          elif name in ['image']:
            c_int_type = self.lmp.c_imageint
          else:
            c_int_type = c_int

          np_int_type = self._ctype_to_numpy_int(c_int_type)

          if dim == 1:
            tmp = self.lmp.extract_atom(name, 0)
            ptr = cast(tmp, POINTER(c_int_type * nelem))
          else:
            tmp = self.lmp.extract_atom(name, 1)
            ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))

          a = np.frombuffer(ptr.contents, dtype=np_int_type)
          a.shape = (nelem, dim)
          return a

        def extract_atom_darray(self, name, nelem, dim=1):
          if dim == 1:
            tmp = self.lmp.extract_atom(name, 2)
            ptr = cast(tmp, POINTER(c_double * nelem))
          else:
            tmp = self.lmp.extract_atom(name, 3)
            ptr = cast(tmp[0], POINTER(c_double * nelem * dim))

          a = np.frombuffer(ptr.contents)
          a.shape = (nelem, dim)
          return a

      self._numpy = LammpsNumpyWrapper(self)
    return self._numpy

  # extract compute info

  def extract_compute(self,id,style,type):
    if id: id = id.encode()
    if type == 0:
      if style > 0: return None
      self.lib.lammps_extract_compute.restype = POINTER(c_double)
      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
      return ptr[0]
    if type == 1:
      self.lib.lammps_extract_compute.restype = POINTER(c_double)
      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
      return ptr
    if type == 2:
      if style == 0:
        self.lib.lammps_extract_compute.restype = POINTER(c_int)
        ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
        return ptr[0]
      else:
        self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
        ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
        return ptr
    return None

  # extract fix info
  # in case of global datum, free memory for 1 double via lammps_free()
  # double was allocated by library interface function

  def extract_fix(self,id,style,type,i=0,j=0):
    if id: id = id.encode()
    if style == 0:
      self.lib.lammps_extract_fix.restype = POINTER(c_double)
      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
      result = ptr[0]
      self.lib.lammps_free(ptr)
      return result
    elif (style == 1) or (style == 2):
      if type == 1:
        self.lib.lammps_extract_fix.restype = POINTER(c_double)
      elif type == 2:
        self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
      else:
        return None
      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
      return ptr
    else:
      return None

  # extract variable info
  # free memory for 1 double or 1 vector of doubles via lammps_free()
  # for vector, must copy nlocal returned values to local c_double vector
  # memory was allocated by library interface function

  def extract_variable(self,name,group,type):
    if name: name = name.encode()
    if group: group = group.encode()
    if type == 0:
      self.lib.lammps_extract_variable.restype = POINTER(c_double)
      ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
      result = ptr[0]
      self.lib.lammps_free(ptr)
      return result
    if type == 1:
      self.lib.lammps_extract_global.restype = POINTER(c_int)
      nlocalptr = self.lib.lammps_extract_global(self.lmp,"nlocal".encode())
      nlocal = nlocalptr[0]
      result = (c_double*nlocal)()
      self.lib.lammps_extract_variable.restype = POINTER(c_double)
      ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
      for i in range(nlocal): result[i] = ptr[i]
      self.lib.lammps_free(ptr)
      return result
    return None

  # return current value of thermo keyword

  def get_thermo(self,name):
    if name: name = name.encode()
    self.lib.lammps_get_thermo.restype = c_double
    return self.lib.lammps_get_thermo(self.lmp,name)

  # return total number of atoms in system

  def get_natoms(self):
    return self.lib.lammps_get_natoms(self.lmp)

  # set variable value
  # value is converted to string
  # returns 0 for success, -1 if failed

  def set_variable(self,name,value):
    if name: name = name.encode()
    if value: value = str(value).encode()
    return self.lib.lammps_set_variable(self.lmp,name,value)

  # reset simulation box size

  def reset_box(self,boxlo,boxhi,xy,yz,xz):
    cboxlo = (3*c_double)(*boxlo)
    cboxhi = (3*c_double)(*boxhi)
    self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)

  # return vector of atom properties gathered across procs
  # 3 variants to match src/library.cpp
  # name = atom property recognized by LAMMPS in atom->extract()
  # type = 0 for integer values, 1 for double values
  # count = number of per-atom valus, 1 for type or charge, 3 for x or f
  # returned data is a 1d vector - doc how it is ordered?
  # NOTE: need to insure are converting to/from correct Python type
  #   e.g. for Python list or NumPy or ctypes

  def gather_atoms(self,name,type,count):
    if name: name = name.encode()
    natoms = self.lib.lammps_get_natoms(self.lmp)
    if type == 0:
      data = ((count*natoms)*c_int)()
      self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
    elif type == 1:
      data = ((count*natoms)*c_double)()
      self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
    else: return None
    return data

  def gather_atoms_concat(self,name,type,count):
    if name: name = name.encode()
    natoms = self.lib.lammps_get_natoms(self.lmp)
    if type == 0:
      data = ((count*natoms)*c_int)()
      self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
    elif type == 1:
      data = ((count*natoms)*c_double)()
      self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
    else: return None
    return data

  def gather_atoms_subset(self,name,type,count,ndata,ids):
    if name: name = name.encode()
    if type == 0:
      data = ((count*ndata)*c_int)()
      self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
    elif type == 1:
      data = ((count*ndata)*c_double)()
      self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
    else: return None
    return data

  # scatter vector of atom properties across procs
  # 2 variants to match src/library.cpp
  # name = atom property recognized by LAMMPS in atom->extract()
  # type = 0 for integer values, 1 for double values
  # count = number of per-atom valus, 1 for type or charge, 3 for x or f
  # assume data is of correct type and length, as created by gather_atoms()
  # NOTE: need to insure are converting to/from correct Python type
  #   e.g. for Python list or NumPy or ctypes

  def scatter_atoms(self,name,type,count,data):
    if name: name = name.encode()
    self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)

  def scatter_atoms_subset(self,name,type,count,ndata,ids,data):
    if name: name = name.encode()
    self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data)

  # create N atoms on all procs
  # N = global number of atoms
  # id = ID of each atom (optional, can be None)
  # type = type of each atom (1 to Ntypes) (required)
  # x = coords of each atom as (N,3) array (required)
  # v = velocity of each atom as (N,3) array (optional, can be None)
  # NOTE: how could we insure are passing correct type to LAMMPS
  #   e.g. for Python list or NumPy, etc
  #   ditto for gather_atoms() above

  def create_atoms(self,n,id,type,x,v,image=None,shrinkexceed=False):
    if id:
      id_lmp = (c_int * n)()
      id_lmp[:] = id
    else:
      id_lmp = id

    if image:
      image_lmp = (c_int * n)()
      image_lmp[:] = image
    else:
      image_lmp = image

    type_lmp = (c_int * n)()
    type_lmp[:] = type
    self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v,image_lmp,
                                 shrinkexceed)

  @property
  def has_exceptions(self):
    """ Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """
    return self.lib.lammps_config_has_exceptions() != 0

  @property
  def has_gzip_support(self):
    return self.lib.lammps_config_has_gzip_support() != 0

  @property
  def has_png_support(self):
    return self.lib.lammps_config_has_png_support() != 0

  @property
  def has_jpeg_support(self):
    return self.lib.lammps_config_has_jpeg_support() != 0

  @property
  def has_ffmpeg_support(self):
    return self.lib.lammps_config_has_ffmpeg_support() != 0

  @property
  def installed_packages(self):
    if self._installed_packages is None:
      self._installed_packages = []
      npackages = self.lib.lammps_config_package_count()
      sb = create_string_buffer(100)
      for idx in range(npackages):
        self.lib.lammps_config_package_name(idx, sb, 100)
        self._installed_packages.append(sb.value.decode())
    return self._installed_packages

# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------

################################################################################
# Alternative Python Wrapper
# Written by Richard Berger <richard.berger@temple.edu>
################################################################################

class OutputCapture(object):
  """ Utility class to capture LAMMPS library output """

  def __init__(self):
    self.stdout_pipe_read, self.stdout_pipe_write = os.pipe()
    self.stdout_fd = 1

  def __enter__(self):
    self.stdout = os.dup(self.stdout_fd)
    os.dup2(self.stdout_pipe_write, self.stdout_fd)
    return self

  def __exit__(self, type, value, tracebac):
    os.dup2(self.stdout, self.stdout_fd)
    os.close(self.stdout)
    os.close(self.stdout_pipe_read)
    os.close(self.stdout_pipe_write)

  # check if we have more to read from the pipe
  def more_data(self, pipe):
    r, _, _ = select.select([pipe], [], [], 0)
    return bool(r)

  # read the whole pipe
  def read_pipe(self, pipe):
    out = ""
    while self.more_data(pipe):
      out += os.read(pipe, 1024).decode()
    return out

  @property
  def output(self):
    return self.read_pipe(self.stdout_pipe_read)


class Variable(object):
  def __init__(self, lammps_wrapper_instance, name, style, definition):
    self.wrapper = lammps_wrapper_instance
    self.name = name
    self.style = style
    self.definition = definition.split()

  @property
  def value(self):
    if self.style == 'atom':
      return list(self.wrapper.lmp.extract_variable(self.name, "all", 1))
    else:
      value = self.wrapper.lmp_print('"${%s}"' % self.name).strip()
      try:
        return float(value)
      except ValueError:
        return value


class AtomList(object):
  def __init__(self, lammps_wrapper_instance):
    self.lmp = lammps_wrapper_instance
    self.natoms = self.lmp.system.natoms
    self.dimensions = self.lmp.system.dimensions

  def __getitem__(self, index):
    if self.dimensions == 2:
        return Atom2D(self.lmp, index + 1)
    return Atom(self.lmp, index + 1)


class Atom(object):
  def __init__(self, lammps_wrapper_instance, index):
    self.lmp = lammps_wrapper_instance
    self.index = index

  @property
  def id(self):
    return int(self.lmp.eval("id[%d]" % self.index))

  @property
  def type(self):
    return int(self.lmp.eval("type[%d]" % self.index))

  @property
  def mol(self):
    return self.lmp.eval("mol[%d]" % self.index)

  @property
  def mass(self):
    return self.lmp.eval("mass[%d]" % self.index)

  @property
  def position(self):
    return (self.lmp.eval("x[%d]" % self.index),
            self.lmp.eval("y[%d]" % self.index),
            self.lmp.eval("z[%d]" % self.index))

  @position.setter
  def position(self, value):
     self.lmp.set("atom", self.index, "x", value[0])
     self.lmp.set("atom", self.index, "y", value[1])
     self.lmp.set("atom", self.index, "z", value[2])

  @property
  def velocity(self):
    return (self.lmp.eval("vx[%d]" % self.index),
            self.lmp.eval("vy[%d]" % self.index),
            self.lmp.eval("vz[%d]" % self.index))

  @velocity.setter
  def velocity(self, value):
     self.lmp.set("atom", self.index, "vx", value[0])
     self.lmp.set("atom", self.index, "vy", value[1])
     self.lmp.set("atom", self.index, "vz", value[2])

  @property
  def force(self):
    return (self.lmp.eval("fx[%d]" % self.index),
            self.lmp.eval("fy[%d]" % self.index),
            self.lmp.eval("fz[%d]" % self.index))

  @property
  def charge(self):
    return self.lmp.eval("q[%d]" % self.index)


class Atom2D(Atom):
  def __init__(self, lammps_wrapper_instance, index):
    super(Atom2D, self).__init__(lammps_wrapper_instance, index)

  @property
  def position(self):
    return (self.lmp.eval("x[%d]" % self.index),
            self.lmp.eval("y[%d]" % self.index))

  @position.setter
  def position(self, value):
     self.lmp.set("atom", self.index, "x", value[0])
     self.lmp.set("atom", self.index, "y", value[1])

  @property
  def velocity(self):
    return (self.lmp.eval("vx[%d]" % self.index),
            self.lmp.eval("vy[%d]" % self.index))

  @velocity.setter
  def velocity(self, value):
     self.lmp.set("atom", self.index, "vx", value[0])
     self.lmp.set("atom", self.index, "vy", value[1])

  @property
  def force(self):
    return (self.lmp.eval("fx[%d]" % self.index),
            self.lmp.eval("fy[%d]" % self.index))


class variable_set:
    def __init__(self, name, variable_dict):
        self._name = name
        array_pattern = re.compile(r"(?P<arr>.+)\[(?P<index>[0-9]+)\]")

        for key, value in variable_dict.items():
            m = array_pattern.match(key)
            if m:
                g = m.groupdict()
                varname = g['arr']
                idx = int(g['index'])
                if varname not in self.__dict__:
                    self.__dict__[varname] = {}
                self.__dict__[varname][idx] = value
            else:
                self.__dict__[key] = value

    def __str__(self):
        return "{}({})".format(self._name, ','.join(["{}={}".format(k, self.__dict__[k]) for k in self.__dict__.keys() if not k.startswith('_')]))

    def __repr__(self):
        return self.__str__()


def get_thermo_data(output):
    """ traverse output of runs and extract thermo data columns """
    if isinstance(output, str):
        lines = output.splitlines()
    else:
        lines = output

    runs = []
    columns = []
    in_run = False
    current_run = {}

    for line in lines:
        if line.startswith("Per MPI rank memory allocation"):
            in_run = True
        elif in_run and len(columns) == 0:
            # first line after memory usage are column names
            columns = line.split()

            current_run = {}

            for col in columns:
                current_run[col] = []

        elif line.startswith("Loop time of "):
            in_run = False
            columns = None
            thermo_data = variable_set('ThermoData', current_run)
            r = {'thermo' : thermo_data }
            runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
        elif in_run and len(columns) > 0:
            values = [float(x) for x in line.split()]

            for i, col in enumerate(columns):
                current_run[col].append(values[i])
    return runs

class PyLammps(object):
  """
  More Python-like wrapper for LAMMPS (e.g., for iPython)
  See examples/ipython for usage
  """

  def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
    if ptr:
      if isinstance(ptr,PyLammps):
        self.lmp = ptr.lmp
      elif isinstance(ptr,lammps):
        self.lmp = ptr
      else:
        self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)
    else:
      self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=None,comm=comm)
    print("LAMMPS output is captured by PyLammps wrapper")
    self._cmd_history = []
    self.runs = []

  def __del__(self):
    if self.lmp: self.lmp.close()
    self.lmp = None

  def close(self):
    if self.lmp: self.lmp.close()
    self.lmp = None

  def version(self):
    return self.lmp.version()

  def file(self,file):
    self.lmp.file(file)

  def write_script(self,filename):
    """ Write LAMMPS script file containing all commands executed up until now """
    with open(filename, "w") as f:
      for cmd in self._cmd_history:
        f.write("%s\n" % cmd)

  def command(self,cmd):
    self.lmp.command(cmd)
    self._cmd_history.append(cmd)

  def run(self, *args, **kwargs):
    output = self.__getattr__('run')(*args, **kwargs)

    if(lammps.has_mpi4py):
      output = self.lmp.comm.bcast(output, root=0) 
    
    self.runs += get_thermo_data(output)
    return output

  @property
  def last_run(self):
    if len(self.runs) > 0:
        return self.runs[-1]
    return None

  @property
  def atoms(self):
    return AtomList(self)

  @property
  def system(self):
    output = self.info("system")
    d = self._parse_info_system(output)
    return namedtuple('System', d.keys())(*d.values())

  @property
  def communication(self):
    output = self.info("communication")
    d = self._parse_info_communication(output)
    return namedtuple('Communication', d.keys())(*d.values())

  @property
  def computes(self):
    output = self.info("computes")
    return self._parse_element_list(output)

  @property
  def dumps(self):
    output = self.info("dumps")
    return self._parse_element_list(output)

  @property
  def fixes(self):
    output = self.info("fixes")
    return self._parse_element_list(output)

  @property
  def groups(self):
    output = self.info("groups")
    return self._parse_groups(output)

  @property
  def variables(self):
    output = self.info("variables")
    vars = {}
    for v in self._parse_element_list(output):
      vars[v['name']] = Variable(self, v['name'], v['style'], v['def'])
    return vars

  def eval(self, expr):
    value = self.lmp_print('"$(%s)"' % expr).strip()
    try:
      return float(value)
    except ValueError:
      return value

  def _split_values(self, line):
    return [x.strip() for x in line.split(',')]

  def _get_pair(self, value):
    return [x.strip() for x in value.split('=')]

  def _parse_info_system(self, output):
    lines = output[6:-2]
    system = {}

    for line in lines:
      if line.startswith("Units"):
        system['units'] = self._get_pair(line)[1]
      elif line.startswith("Atom style"):
        system['atom_style'] = self._get_pair(line)[1]
      elif line.startswith("Atom map"):
        system['atom_map'] = self._get_pair(line)[1]
      elif line.startswith("Atoms"):
        parts = self._split_values(line)
        system['natoms'] = int(self._get_pair(parts[0])[1])
        system['ntypes'] = int(self._get_pair(parts[1])[1])
        system['style'] = self._get_pair(parts[2])[1]
      elif line.startswith("Kspace style"):
        system['kspace_style'] = self._get_pair(line)[1]
      elif line.startswith("Dimensions"):
        system['dimensions'] = int(self._get_pair(line)[1])
      elif line.startswith("Orthogonal box"):
        system['orthogonal_box'] = [float(x) for x in self._get_pair(line)[1].split('x')]
      elif line.startswith("Boundaries"):
        system['boundaries'] = self._get_pair(line)[1]
      elif line.startswith("xlo"):
        keys, values = [self._split_values(x) for x in self._get_pair(line)]
        for key, value in zip(keys, values):
          system[key] = float(value)
      elif line.startswith("ylo"):
        keys, values = [self._split_values(x) for x in self._get_pair(line)]
        for key, value in zip(keys, values):
          system[key] = float(value)
      elif line.startswith("zlo"):
        keys, values = [self._split_values(x) for x in self._get_pair(line)]
        for key, value in zip(keys, values):
          system[key] = float(value)
      elif line.startswith("Molecule type"):
        system['molecule_type'] = self._get_pair(line)[1]
      elif line.startswith("Bonds"):
        parts = self._split_values(line)
        system['nbonds'] = int(self._get_pair(parts[0])[1])
        system['nbondtypes'] = int(self._get_pair(parts[1])[1])
        system['bond_style'] = self._get_pair(parts[2])[1]
      elif line.startswith("Angles"):
        parts = self._split_values(line)
        system['nangles'] = int(self._get_pair(parts[0])[1])
        system['nangletypes'] = int(self._get_pair(parts[1])[1])
        system['angle_style'] = self._get_pair(parts[2])[1]
      elif line.startswith("Dihedrals"):
        parts = self._split_values(line)
        system['ndihedrals'] = int(self._get_pair(parts[0])[1])
        system['nangletypes'] = int(self._get_pair(parts[1])[1])
        system['dihedral_style'] = self._get_pair(parts[2])[1]
      elif line.startswith("Impropers"):
        parts = self._split_values(line)
        system['nimpropers'] = int(self._get_pair(parts[0])[1])
        system['nimpropertypes'] = int(self._get_pair(parts[1])[1])
        system['improper_style'] = self._get_pair(parts[2])[1]

    return system

  def _parse_info_communication(self, output):
    lines = output[6:-3]
    comm = {}

    for line in lines:
      if line.startswith("MPI library"):
        comm['mpi_version'] = line.split(':')[1].strip()
      elif line.startswith("Comm style"):
        parts = self._split_values(line)
        comm['comm_style'] = self._get_pair(parts[0])[1]
        comm['comm_layout'] = self._get_pair(parts[1])[1]
      elif line.startswith("Processor grid"):
        comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
      elif line.startswith("Communicate velocities for ghost atoms"):
        comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
      elif line.startswith("Nprocs"):
        parts = self._split_values(line)
        comm['nprocs'] = int(self._get_pair(parts[0])[1])
        comm['nthreads'] = int(self._get_pair(parts[1])[1])
    return comm

  def _parse_element_list(self, output):
    lines = output[6:-3]
    elements = []

    for line in lines:
      element_info = self._split_values(line.split(':')[1].strip())
      element = {'name': element_info[0]}
      for key, value in [self._get_pair(x) for x in element_info[1:]]:
        element[key] = value
      elements.append(element)
    return elements

  def _parse_groups(self, output):
    lines = output[6:-3]
    groups = []
    group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")

    for line in lines:
      m = group_pattern.match(line.split(':')[1].strip())
      group = {'name': m.group('name'), 'type': m.group('type')}
      groups.append(group)
    return groups

  def lmp_print(self, s):
    """ needed for Python2 compatibility, since print is a reserved keyword """
    return self.__getattr__("print")(s)

  def __dir__(self):
    return ['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style',
    'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute',
    'create_atoms', 'create_box', 'delete_atoms', 'delete_bonds', 'dielectric',
    'dihedral_coeff', 'dihedral_style', 'dimension', 'dump', 'fix', 'fix_modify',
    'group', 'improper_coeff', 'improper_style', 'include', 'kspace_modify',
    'kspace_style', 'lattice', 'mass', 'minimize', 'min_style', 'neighbor',
    'neigh_modify', 'newton', 'nthreads', 'pair_coeff', 'pair_modify',
    'pair_style', 'processors', 'read', 'read_data', 'read_restart', 'region',
    'replicate', 'reset_timestep', 'restart', 'run', 'run_style', 'thermo',
    'thermo_modify', 'thermo_style', 'timestep', 'undump', 'unfix', 'units',
    'variable', 'velocity', 'write_restart']

  def __getattr__(self, name):
    def handler(*args, **kwargs):
      cmd_args = [name] + [str(x) for x in args]

      with OutputCapture() as capture:
        self.command(' '.join(cmd_args))
        output = capture.output

      if 'verbose' in kwargs and kwargs['verbose']:
        print(output)

      lines = output.splitlines()

      if len(lines) > 1:
        return lines
      elif len(lines) == 1:
        return lines[0]
      return None

    return handler


class IPyLammps(PyLammps):
  """
  iPython wrapper for LAMMPS which adds embedded graphics capabilities
  """

  def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
    super(IPyLammps, self).__init__(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)

  def image(self, filename="snapshot.png", group="all", color="type", diameter="type",
            size=None, view=None, center=None, up=None, zoom=1.0):
    cmd_args = [group, "image", filename, color, diameter]

    if size:
      width = size[0]
      height = size[1]
      cmd_args += ["size", width, height]

    if view:
      theta = view[0]
      phi = view[1]
      cmd_args += ["view", theta, phi]

    if center:
      flag = center[0]
      Cx = center[1]
      Cy = center[2]
      Cz = center[3]
      cmd_args += ["center", flag, Cx, Cy, Cz]

    if up:
      Ux = up[0]
      Uy = up[1]
      Uz = up[2]
      cmd_args += ["up", Ux, Uy, Uz]

    if zoom:
      cmd_args += ["zoom", zoom]

    cmd_args.append("modify backcolor white")

    self.write_dump(*cmd_args)
    from IPython.core.display import Image
    return Image('snapshot.png')

  def video(self, filename):
    from IPython.display import HTML
    return HTML("<video controls><source src=\"" + filename + "\"></video>")